Biological monitoring focuses on living organisms that are exposed to various water quality stressors or may respond to an improvement in water quality conditions. Depending on the system and the stressor, monitoring may focus on fish, birds, large aquatic plants, periphyton, microscopic algae, or aquatic macroinvertebrates, or even on specific biological pathways and processes such as the rate at which oxygen is generated during photosynthesis. Biological monitoring has become increasingly important because of the value of “indicator species,” which are organisms or groups of organisms that respond in a characteristic way to types of pollutants or other stressors. A comparison of the relative abundance of these indicator species to what is expected in comparable unpolluted water bodies (reference streams) can indicate ongoing or past pollution, even when it is not evident in water column samples. Often, support of aquatic life is the beneficial use impaired in a water body, and biological monitoring provides a direct measure of this use.

Some types of biological samples may be relatively simple to collect but may require expensive equipment. For example, the fluorescence of chlorophyll in a water column measures light emitted from chlorophyll molecules and is therefore correlated to the amount of plant biomass in a water body. This is relatively easy to measure but requires special equipment. Other types of organisms, such as macroinvertebrates or periphyton, are relatively easy and inexpensive to collect, but processing these samples and identifying to the appropriate taxonomic level may be time consuming, may be costly, and may require special expertise.

Organisms may be distributed quite unevenly in a water body, which presents a challenge to collecting a representative sample. Different habitats (riffles, pools, nearshore, backwaters) may also support entirely different plant and animal communities, so collecting a representative sample may require sampling in multiple areas. Temporal changes in the size and distribution of organisms must also be accounted for. Many plants die back during winter months. Aquatic insects often “drift” so are present in the water column only at night, and zooplankton and fish may “vertically migrate” from deep waters to the surface over a 24-hour period.

Detecting change in biological communities does not necessarily indicate changes in the pollutant or stressor of concern. The linkage between changes in the biological samples and the pollutant of concern must be well understood.